bioconductor: iPath | Projects | Ecosyste.ms: Papers

10.3389/fmicb.2020.557253

Sixty-One Volatiles Have Phylogenetic Signals Across Bacterial Domain and Fungal Kingdom
Cited by: 16
Author(s): Moamen M. Elmassry, Mohamed A. Farag, Robert Preißner, Björn-Oliver Gohlke, Birgit Piechulla, Marie Chantal Lemfack
Software Mentions: 9
Published: about 4 years ago

10.1186/s13742-015-0077-2

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future
Cited by: 83
Author(s): Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Θεοδόσιος Θεοδοσίου, Anton J. Enright, Ioannis Iliopoulos
Software Mentions: 7
Published: about 9 years ago

10.3389/fgene.2019.00904

Advances and Challenges in Metatranscriptomic Analysis
Cited by: 217
Author(s): Migun Shakya, Chien‐Chi Lo, Patrick Chain
Software Mentions: 6
Published: about 5 years ago

10.1016/j.cels.2018.08.001

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts
Cited by: 77
Author(s): Aleksej Zelezniak, Jakob Vowinckel, Floriana Capuano, Christoph B. Messner, Vadim Demichev, Nicole Polowsky, Michael Mülleder, Stephan Kamrad, Bernd Klaus, Markus A. Keller, Markus Ralser
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-019-41452-2

Using Bacterial Transcriptomics to Investigate Targets of Host-Bacterial Interactions in Caenorhabditis elegans
Cited by: 21
Author(s): Jason P. Chan, Justin Wright, Hoi Tong Wong, Anastasia Ardasheva, Jamey T. Brumbaugh, Christopher J. McLimans, Regina Lamendella
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-015-0146-x

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality
Cited by: 91
Author(s): Yue Jiang, Xuejian Xiong, Jayne S. Danska, John Parkinson
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2164-15-71

Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian
Cited by: 37
Author(s): Derek Stefanik, Tristan Lubinski, Brian R. Granger, Allyson L. Byrd, Adam M. Reitzel, Lukas DeFilippo, Allison Lorenc, John R. Finnerty
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pcbi.1009105

Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis
Cited by: 40
Author(s): Cecilia Wieder, Clément Frainay, Nathalie Poupin, Pablo Rodríguez-Mier, Florence Vinson, Juliette Cooke, Rachel Lai, Jacob G. Bundy, Fabien Jourdan, Timothy M. D. Ebbels
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2021.736411

Transcriptomic Analysis of Pediococcus pentosaceus Reveals Carbohydrate Metabolic Dynamics Under Lactic Acid Stress
Cited by: 2
Author(s): Dong Han, Qiaojuan Yan, Jun Li, Zhengqiang Jiang, Shanchao Yang
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pgen.1007357

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti
Cited by: 48
Author(s): George C. diCenzo, Alex B. Benedict, Marco Fondi, Graham C. Walker, Turlough M. Finan, Alessio Mengoni, Joel S. Griffitts
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms17101749

Transcriptome Sequencing and De Novo Assembly of Golden Cuttlefish Sepia esculenta Hoyle
Cited by: 14
Author(s): Changlin Liu, Fazhen Zhao, Jing Yan, Chunsheng Liu, Siwei Liu, Siqing Chen
Software Mentions: 3
Published: about 8 years ago

10.1128/mSystems.00441-21

Metabolic Features of Ganjang (a Korean Traditional Soy Sauce) Fermentation Revealed by Genome-Centered Metatranscriptomics
Cited by: 18
Author(s): Byung Hee Chun, Dong Han, Hyung Min Kim, Dongbin Park, Da Min Jeong, Hyun Ah Kang, Che Ok Jeon
Software Mentions: 3
Published: about 3 years ago

10.1186/s12870-021-03124-0

The role of strigolactones in P deficiency induced transcriptional changes in tomato roots
Cited by: 17
Author(s): Yanting Wang, Hernando G. Suárez Duran, Jan C. van Haarst, Elio Schijlen, Carolien Ruyter-Spira, Marnix H. Medema, Lemeng Dong, Harro J. Bouwmeester
Software Mentions: 3
Published: over 3 years ago

10.1186/s12863-020-00945-0

Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis
Cited by: 5
Author(s): Zhaohui Cai, Qiongyu Guo, Zhichao Yao, Wenping Zheng, Junfei Xie, Shuai Bai, Hongyu Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-15-563

Hemolymph proteome changes during worker brood development match the biological divergences between western honey bees (Apis mellifera) and eastern honey bees (Apis cerana)
Cited by: 28
Author(s): Feng Mao, Haitham Ramadan, Bin Han, Fang Yu, Jianke Li
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0161987

De Novo Assembly and Transcriptome Analysis of Bulb Onion (Allium cepa L.) during Cold Acclimation Using Contrasting Genotypes
Cited by: 25
Author(s): Jeongsukhyeon Han, Senthil Kumar Thamilarasan, Sathishkumar Natarajan, Jong-In Park, Mi-Young Chung, Ill–Sup Nou
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2019.00325

Proteomic Analysis of Lactobacillus nagelii in the Presence of Saccharomyces cerevisiae Isolated From Water Kefir and Comparison With Lactobacillus hordei
Cited by: 16
Author(s): Julia Bechtner, Di Xu, Jürgen Behr, Christina Ludwig, Rudi F. Vogel
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-015-0585-1

PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways
Cited by: 10
Author(s): Yongnan Zhu, Liang Sun, Alexander Garbarino, Carl J. Schmidt, Jinglong Fang, Jian Chen
Software Mentions: 3
Published: over 9 years ago

10.1186/s12951-021-01047-4

An atherosclerotic plaque-targeted single-chain antibody for MR/NIR-II imaging of atherosclerosis and anti-atherosclerosis therapy
Cited by: 15
Author(s): Liwei Zhang, Sheng Xue, Feng Ren, Si-Yang Huang, Ruizhi Zhou, Yu Wang, Chunxiao Zhou, Zhen Li
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2021.651282

Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas
Cited by: 46
Author(s): Olga V. Mavrodi, Janiece R. McWilliams, Jacob Peter, Anna Berim, Karl A. Hassan, Liam D. H. Elbourne, Melissa K. LeTourneau, David R. Gang, Ian T. Paulsen, David M. Weller, Linda S. Thomashow, Alex S. Flynt, Dmitri V. Mavrodi
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-020-06827-0

Transcriptome analysis reveals a molecular understanding of nicotinamide and butyrate sodium on meat quality of broilers under high stocking density
Cited by: 10
Author(s): Yuqin Wu, Youli Wang, Dafei Yin, Tahir Mahmood, Jianmin Yuan
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2020.01043

Comparison of Transcriptome Profiles of the Fungus Botrytis cinerea and Insect Pest Bradysia odoriphaga in Response to Benzothiazole
Cited by: 9
Author(s): Kaidi Cui, Yunhe Zhao, Lifei He, Jinfeng Ding, Beixing Li, Wei Mu, Feng Liu
Software Mentions: 3
Published: over 4 years ago

10.1186/s40064-016-3728-6

Characterization of saliva microbiota’s functional feature based on metagenomic sequencing
Cited by: 13
Author(s): Fang Yang, Kang Ning, Xiaowei Zeng, Qian Zhou, Xiaoquan Su, Xiao Yuan
Software Mentions: 2
Published: almost 8 years ago

10.18632/aging.202969

Ketogenic diet-mediated steroid metabolism reprogramming improves the immune microenvironment and myelin growth in spinal cord injury rats according to gene and co-expression network analyses
Cited by: 4
Author(s): Hong Zeng, Yao Lu, Meng-jie Huang, Yanyan Yang, Huayi Xing, Xiao-xie Liu, Mouwang Zhou
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-12-176

Web-based metabolic network visualization with a zooming user interface
Cited by: 31
Author(s): Mario Latendresse, Peter D. Karp
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-11-703

Gene discovery in the horned beetle Onthophagus taurus
Cited by: 38
Author(s): Jeong Hyeon Choi, Teiya Kijimoto, Emilie C. Snell‐Rood, Hongseok Tae, Youngik Yang, Armin P. Moczek, Justen Andrews
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2164-13-284

Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct
Cited by: 85
Author(s): Hao Hu, Pradip K. Bandyopadhyay, Baldomero M. Olivera, Mark Yandell
Software Mentions: 2
Published: over 12 years ago

10.1186/s12870-015-0508-3

Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt
Cited by: 53
Author(s): Jie‐Yin Chen, Jinqun Huang, Nan‐Yang Li, Xuefeng Ma, Jinlong Wang, Chuan Liu, Yongfeng Liu, Yong Liang, Yuming Bao, Xiaofeng Dai
Software Mentions: 2
Published: over 9 years ago

10.1093/bioinformatics/btz245

FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization
Cited by: 13
Author(s): Youssef Darzi, Yuta Yamate, Takuji Yamada
Software Mentions: 2
Published: over 5 years ago

10.1186/s13068-018-1331-5

Comparative transcriptome analyses of oleaginous Botryococcus braunii race A reveal significant differences in gene expression upon cobalt enrichment
Cited by: 9
Author(s): Pengfei Cheng, Chengxu Zhou, Yan Wu, Zhihui Xu, Jilin Xu, Dongqing Zhou, Yinghui Zhang, Haizhen Wu, Xuezhi Zhang, Tianzhong Liu, Ming Tang, Yang Qiyong, Xiaojun Yan, Jianhua Fan
Software Mentions: 2
Published: almost 6 years ago

10.1093/bib/bbz067

Closing the gap between formats for storing layout information in systems biology
Cited by: 11
Author(s): David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
Software Mentions: 2
Published: over 5 years ago

10.3390/metabo11020064

Pathway Tools Visualization of Organism-Scale Metabolic Networks
Cited by: 8
Author(s): Suzanne M. Paley, Richard Billington, James A. Herson, Markus Krummenacker, Peter D. Karp
Software Mentions: 2
Published: almost 4 years ago

10.1080/21505594.2017.1423188

Boosted TCA cycle enhances survival of zebrafish to Vibrio alginolyticus infection
Cited by: 53
Author(s): Meisongzhu Yang, Zhi-xue Cheng, Ming Jiang, Zao-hai Zeng, Bo Peng, Xuan‐xian Peng, Hui Li
Software Mentions: 2
Published: over 6 years ago

10.1080/21505594.2020.1750123

Malate enhances survival of zebrafish against Vibrio alginolyticus infection in the same manner as taurine
Cited by: 35
Author(s): Meisongzhu Yang, Di Xu, Dai-xiao Yang, Lü Li, Xuan‐xian Peng, Zhuang‐Gui Chen, Hui Li
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pbio.1002530

Modelling the Structure and Dynamics of Biological Pathways
Cited by: 27
Author(s): Laura O’Hara, Alessandra Livigni, Thanos Theo, Benjamin Boyer, Tim Angus, Derek W. Wright, Sz-Hau Chen, Sobia Raza, Mark W. Barnett, Paul Digard, Lee B. Smith, Tom C. Freeman
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1002558

Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides
Cited by: 75
Author(s): Tara A. Gianoulis, Michael Griffin, Daniel Spakowicz, Brian F. Dunican, Cambria J. Alpha, Andrea Sboner, A. Michael Sismour, Chinnappa D. Kodira, Michael Egholm, George M. Church, Mark Gerstein, Scott A. Strobel
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0226567

The treeness of the tree of historical trees of life
Cited by: 2
Author(s): Marie Fisler, Cédric Crémière, Pierre Darlu, Guillaume Lecointre
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0126967

FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data
Cited by: 28
Author(s): Takuro Uchiyama, Masahiro Irie, Hiroshi Mori, Ken Kurokawa, Takuji Yamada
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0007710

Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API
Cited by: 80
Author(s): Nobuaki Kono, Kazuharu Arakawa, Ryu Ogawa, Nobuhiro Kido, Kazuki Oshita, Keita Ikegami, Satoshi Tamaki, Masaru Tomita
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0029913

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions
Cited by: 174
Author(s): Carolin A. Kolmeder, Mark de Been, Janne Nikkilä, Ilja Ritamo, Jaana Mättö, Leena Valmu, Jarkko Salojärvi, Airi Palva, Anne Salonen, Willem M. de Vos
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0072361

PhenoTimer: Software for the Visual Mapping of Time-Resolved Phenotypic Landscapes
Cited by: 1
Author(s): Maria Secrier, Reinhard Schneider
Software Mentions: 2
Published: over 11 years ago

10.1186/gb-2013-14-11-r123

Metabolic reprogramming by viruses in the sunlit and dark ocean
Cited by: 188
Author(s): Bonnie Hurwitz, Steven J. Hallam, Matthew B. Sullivan
Software Mentions: 2
Published: almost 12 years ago

10.1038/s41598-018-22093-3

Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni
Cited by: 16
Author(s): Mariana Boroni, Michael Sammeth, Sandra Grossi Gava, Natasha Andressa Nogueira Jorge, Andréa Mara Macedo, Carlos Renato Machado, Marina Moraes Mourão, Glória Regina Franco
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.00020-17

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium
Cited by: 45
Author(s): Roshan Kumar, Helianthous Verma, Shazia Haider, Abhay Bajaj, Utkarsh Sood, Kalaiarasan Ponnusamy, Shekhar Nagar, Mallikarjun Shakarad, Ram Krishan Negi, Yogendra Singh, Jitendra P. Khurana, Jack A. Gilbert, Rup Lal
Software Mentions: 2
Published: over 7 years ago

10.1186/s12876-016-0534-0

Cirrhosis related functionality characteristic of the fecal microbiota as revealed by a metaproteomic approach
Cited by: 32
Author(s): Xiao Wei, Shan Jiang, Yuye Chen, Xiangna Zhao, Huan Li, Weihua Lin, Boxing Li, Xuesong Wang, Jing Yuan, Yansong Sun
Software Mentions: 1
Published: about 8 years ago

10.1128/mSystems.00694-21

Enhanced Biosynthesis of Fatty Acids Is Associated with the Acquisition of Ciprofloxacin Resistance in Edwardsiella tarda
Cited by: 23
Author(s): Yubin Su, Su-fang Kuang, Jin-zhou Ye, Jian-jun Tao, Hui Li, Xuan‐xian Peng, Bo Peng
Software Mentions: 1
Published: about 3 years ago

10.1200/JGO.2015.002162

Implementation and Validation of Telepathology Triage at Cancer Referral Center in Rural Rwanda
Cited by: 31
Author(s): Tharcisse Mpunga, Bethany Hedt‐Gauthier, Neo Tapela, Irénée Nshimiyimana, Gaspard Muvugabigwi, Natalie Pritchett, L. Greenberg, Origene Benewe, David S. Shulman, James R. Pepoon, Lawrence N. Shulman, Danny A. Milner
Software Mentions: 1
Published: over 8 years ago

10.1200/JGO.17.00081

Decreasing Histology Turnaround Time Through Stepwise Innovation and Capacity Building in Rwanda
Cited by: 9
Author(s): Gaspard Muvugabigwi, Irénée Nshimiyimana, L. Greenberg, Emmanuel Hakizimana, Deo Ruhangaza, Origene Benewe, Kiran Bhai, James R. Pepoon, Alexandra Fehr, Paul H. Park, John Butonzi, Cyprien Shyirambere, Alexis Manirakiza, Christian Rusangwa, Danny A. Milner, Tharcisse Mpunga, Lawrence N. Shulman
Software Mentions: 1
Published: almost 6 years ago

10.3390/microorganisms8030327

Metabolomics Analysis Reveals the Alkali Tolerance Mechanism in Puccinellia tenuiflora Plants Inoculated with Arbuscular Mycorrhizal Fungi
Cited by: 27
Author(s): Chunxue Yang, Wenna Zhao, Yingnan Wang, Liang Zhang, Shouchen Huang, Jixiang Lin
Software Mentions: 1
Published: over 4 years ago

10.1093/database/bax026

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data
Cited by: 14
Author(s): Mathurin Dorel, Éric Viara, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein
Software Mentions: 1
Published: almost 8 years ago

10.1186/1746-1596-1-33

Static telepathology in cancer institute of Tehran university: report of the first academic experience in Iran
Cited by: 13
Author(s): Afshin Abdirad, Babak Sarrafpour, Siavash Ghaderi‐Sohi
Software Mentions: 1
Published: about 18 years ago

10.1016/j.ymben.2017.02.010

Metabolic anchor reactions for robust biorefining
Cited by: 13
Author(s): Paula Jouhten, Jaime Huerta-Cepas, Peer Bork, Kiran Raosaheb Patil
Software Mentions: 1
Published: over 7 years ago

10.3389/fimmu.2017.01706

Edwardsiella tarda Tunes Tricarboxylic Acid Cycle to Evade Complement-Mediated Killing
Cited by: 34
Author(s): Zhi-xue Cheng, Qiyang Gong, Zhe Wang, Zhuang‐Gui Chen, Jin-zhou Ye, Jun Li, Jie Wang, Meisongzhu Yang, Xi Ling, Bo Peng
Software Mentions: 1
Published: almost 7 years ago

10.3389/fimmu.2021.682724

Myo-Inositol Restores Tilapia’s Ability Against Infection by Aeromonas sobria in Higher Water Temperature
Cited by: 6
Author(s): Meisongzhu Yang, Ming Jiang, Xuan‐xian Peng, Hui Li
Software Mentions: 1
Published: about 3 years ago

10.3389/fmicb.2021.698286

DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data
Cited by: 15
Author(s): Chun-Xu Xue, Heyu Lin, Xiaoyu Zhu, Jiwen Liu, Yunhui Zhang, Gary Rowley, Jonathan D. Todd, Meng Li, Xiaohua Zhang
Software Mentions: 1
Published: over 3 years ago

10.1186/1472-6955-12-6

Experience of nurses with using eHealth in Gilgit-Baltistan, Pakistan: a qualitative study in primary and secondary healthcare
Cited by: 8
Author(s): Saleema Gulzar, Shariq Khoja, Afroz Sajwani
Software Mentions: 1
Published: over 11 years ago

10.3389/fmicb.2017.00797

Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention
Cited by: 82
Author(s): Chunlong Mu, Yu‐Xiang Yang, Yong Su, Erwin G. Zoetendal, Weiyun Zhu
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2018.01717

Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas
Cited by: 36
Author(s): Sheng Yang, Xin Gao, Jianghong Meng, Anyun Zhang, Yingmin Zhou, Liang Ma, Bei Li, Wenwen Deng, Lan Jin, Sumei Zhao, Daifu Wu, Yongguo He, Caiwu Li, Shuliang Liu, Yan Huang, Hemin Zhang, Likou Zou
Software Mentions: 1
Published: over 6 years ago

10.3389/fmicb.2021.588025

Active Microbiome Structure and Functional Analyses of Freshwater Benthic Biofilm Samples Influenced by RNA Extraction Methods
Cited by: 1
Author(s): Yuan Yao, Subramanya Rao, Olivier Habimana
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-13-242

An elm EST database for identifying leaf beetle egg-induced defense genes
Cited by: 28
Author(s): Kerstin Büchel, Eric T. McDowell, Will Nelson, Anne Descour, Jonathan Gershenzon, Monika Hilker, Carol Soderlund, David R. Gang, T. M. Fenning, Torsten Meiners
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-015-1428-1

Transcriptomic analyses reveal species-specific light-induced anthocyanin biosynthesis in chrysanthemum
Cited by: 75
Author(s): Yanbin Hong, Xingjiao Tang, Hua He, Zhongwei Yuan, Silan Dai
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-14-530

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
Cited by: 111
Author(s): Milkha M. Leimena, Javier Ramiro-García, Mark Davids, Bartholomeus van den Bogert, Hauke Smidt, Eddy J. Smid, Jos Boekhorst, Erwin G. Zoetendal, Peter J. Schaap, Michiel Kleerebezem
Software Mentions: 1
Published: over 11 years ago

10.3389/fmicb.2018.00029

Alanine Enhances Aminoglycosides-Induced ROS Production as Revealed by Proteomic Analysis
Cited by: 66
Author(s): Jin-zhou Ye, Yubin Su, Xiangmin Lin, Shi‐shi Lai, Wanxin Li, Farman Ali, Jun Zheng, Bo Peng
Software Mentions: 1
Published: almost 7 years ago

10.3389/fmicb.2013.00092

Design and development of synthetic microbial platform cells for bioenergy
Cited by: 32
Author(s): Sang Jun Lee, Sang Jae Lee, Dong Woo Lee
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-13-S7-S10

An analysis of the transcriptome of Teladorsagia circumcincta: its biological and biotechnological implications
Cited by: 16
Author(s): Ranjeeta Menon, Robin B. Gasser, Makedonka Mitreva, Shoba Ranganathan
Software Mentions: 1
Published: almost 12 years ago

10.3389/fmolb.2021.644957

Succinate Promotes Phagocytosis of Monocytes/Macrophages in Teleost Fish
Cited by: 14
Author(s): Dai-xiao Yang, Hao Yang, Yunchao Cao, Ming Jiang, Jun Zheng, Bo Peng
Software Mentions: 1
Published: over 3 years ago

10.3389/fphar.2019.01146

Synergistic Combination of Polymyxin B and Enrofloxacin Induced Metabolic Perturbations in Extensive Drug-Resistant Pseudomonas aeruginosa
Cited by: 16
Author(s): Lin Ye, Mei‐Ling Han, Jinxin Zhao, Yan Zhu, Gauri G. Rao, Alan Forrest, Jiangning Song, Keith S. Kaye, Paul J. Hertzog, Anthony W. Purcell, Darren J. Creek, Qi Tony Zhou, Tony Velkov, Jian Li
Software Mentions: 1
Published: about 5 years ago

10.3389/fphys.2021.633964

Dietary Beta-Hydroxy-Beta-Methyl Butyrate Supplementation Affects Growth, Carcass Characteristics, Meat Quality, and Serum Metabolomics Profile in Broiler Chickens
Cited by: 11
Author(s): Zhiyi Tang, Bo Song, Chunyan Zheng, Jie Zheng, Yulong Yin, Jiashun Chen
Software Mentions: 1
Published: almost 4 years ago

10.3389/fpls.2020.580330

Genome-Wide Identification of Dickeya solani Transcriptional Units Up-Regulated in Response to Plant Tissues From a Crop-Host Solanum tuberosum and a Weed-Host Solanum dulcamara
Cited by: 10
Author(s): Robert Czajkowski, Jakub Fikowicz-Krośko, Tomasz Maciąg, Łukasz Rąbalski, Paulina Czaplewska, Sylwia Jafra, Malwina Richert, Marta Krychowiak-Maśnicka, Nicole Hugouvieux‐Cotte‐Pattat
Software Mentions: 1
Published: about 4 years ago

10.3389/fpls.2017.01429

Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species
Cited by: 17
Author(s): Linhong Teng, Xiao Fan, Dong Xu, Xiaowen Zhang, Thomas Möck, Naihao Ye
Software Mentions: 1
Published: over 7 years ago

10.3389/fpls.2018.00004

Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits
Cited by: 39
Author(s): Thangasamy Saminathan, Marleny González García, Bandana Ghimire, Carlos M. Rodríguez López, Abiodun Bodunrin, Padma Nimmakayala, Venkata Lakshmi Abburi, Amnon Levi, Nagamani Balagurusamy, Umesh K. Reddy
Software Mentions: 1
Published: almost 7 years ago

10.3389/fpubh.2019.00264

Telepathology in Low Resource African Settings
Cited by: 15
Author(s): Nnamdi Orah, Olorunda Rotimi
Software Mentions: 1
Published: about 5 years ago

10.1186/gb-2013-14-2-r19

Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes
Cited by: 77
Author(s): Cecilia Alsmark, Peter G. Foster, Thomas Sicheritz-Pontén, Sirintra Nakjang, T. Martin Embley, Robert P. Hirt
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12885-020-07336-9

Alteration of plasma metabolites associated with chemoradiosensitivity in esophageal squamous cell carcinoma via untargeted metabolomics approach
Cited by: 9
Author(s): Yaowen Zhang, Jianpo Wang, Ning Dai, Peng Han, Jian Li, Jiangman Zhao, Weilan Yuan, Jiahuan Zhou, Fuyou Zhou
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2164-12-S4-S3

Preimplantation development regulatory pathway construction through a text-mining approach
Cited by: 6
Author(s): Elisa Donnard, Adriano Barbosa-Silva, Rafael Lucas Muniz Guedes, Gabriel R. Fernandes, Henrique Velloso, Matthew J. Kohn, Miguel A. Andrade‐Navarro, José Miguel Ortega
Software Mentions: 1
Published: almost 13 years ago

10.1002/rcm.5245

Pathos: A web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry
Cited by: 49
Author(s): David P. Leader, Karl Burgess, Darren J. Creek, Michael P. Barrett
Software Mentions: 1
Published: about 13 years ago

10.1038/srep11867

Dynamic transcriptome analysis and volatile profiling of Gossypium hirsutum in response to the cotton bollworm Helicoverpa armigera
Cited by: 38
Author(s): Xianjin Huang, Jie‐Yin Chen, Haijun Xiao, Yutao Xiao, Juan Wu, Junxiang Wu, Jing‐Jiang Zhou, Yongjun Zhang, Yong Guo
Software Mentions: 1
Published: over 9 years ago

10.1038/srep17450

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria
Cited by: 63
Author(s): Haikang Shen, Fuqiang Ye, Lu Xie, Jianfeng Yang, Zhen Li, Peisong Xu, Fei Meng, Lei Li, Ying Chen, Xiaochen Bo, Ming Ni, Xiaofeng Zhang
Software Mentions: 1
Published: almost 9 years ago

10.1038/srep21796

Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment
Cited by: 11
Author(s): Hyun Mi Jin, Hye Im Jeong, Kyung Hyun Kim, Yoonsoo Hahn, Eugene L. Madsen, Che Ok Jeon
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-12016-z

Pan-genomic and transcriptomic analyses of Leuconostoc mesenteroides provide insights into its genomic and metabolic features and roles in kimchi fermentation
Cited by: 50
Author(s): Byung Hee Chun, Kyung Hyun Kim, Hye Hee Jeon, Se Hee Lee, Che Ok Jeon
Software Mentions: 1
Published: about 7 years ago

10.3390/ijms22147346

Pectobacterium parmentieri SCC 3193 Mutants with Altered Synthesis of Cell Surface Polysaccharides Are Resistant to N4-Like Lytic Bacteriophage ϕA38 (vB_Ppp_A38) but Express Decreased Virulence in Potato (Solanum tuberosum L.) Plants
Cited by: 6
Author(s): Przemysław Bartnik, Sylwia Jafra, Magdalena Narajczyk, Paulina Czaplewska, Robert Czajkowski
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-018-33261-w

Genome-wide analysis of horizontally acquired genes in the genus Mycobacterium
Cited by: 20
Author(s): Arup Panda, Michel Drancourt, Tamir Tuller, Pierre Pontarotti
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-017-4413-z

Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure
Cited by: 18
Author(s): Stephen P. LaVoie, Anne O. Summers
Software Mentions: 1
Published: almost 7 years ago

10.4102/ajlm.v2i1.82

Haematopathology diagnosis: Role of multidisciplinary training workshops
Cited by: 0
Author(s): Jessie Githanga, Nina Hurwitz
Software Mentions: 1
Published: over 11 years ago

10.1186/s40793-017-0256-0

Complete genome sequence of Leuconostoc suionicum DSM 20241T provides insights into its functional and metabolic features
Cited by: 10
Author(s): Byung Hee Chun, Se Hee Lee, Hye Hee Jeon, Dong Ho Kim, Che Ok Jeon
Software Mentions: 1
Published: over 7 years ago

10.1038/s41398-021-01344-4

SHR/NCrl rats as a model of ADHD can be discriminated from controls based on their brain, blood, or urine metabolomes
Cited by: 3
Author(s): Camille Dupuy, Pierre Castelnau, Sylvie Mavel, Antoine Lefèvre, Lydie Nadal-Desbarats, Sylvie Bodard, Julie Busson, Diane Dufour‐Rainfray, Hélène Blasco, Patrick Emond, Laurent Galineau
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-11-S1-S38

Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways
Cited by: 28
Author(s): Adi Mano, Tamir Tuller, Oded Béjà, Ron Y. Pinter
Software Mentions: 1
Published: almost 15 years ago

10.1039/d1mo00017a

Metabolomics in infectious diseases and drug discovery
Cited by: 48
Author(s): Vivian Tounta, Yi Liu, Ashleigh Cheyne, Gérald Larrouy-Maumus
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0012459

Gut Microbial Gene Expression in Mother-Fed and Formula-Fed Piglets
Cited by: 95
Author(s): Valeriy Poroyko, James R. White, Mei Wang, Sharon M. Donovan, John C. Alverdy, Donald C. Liu, Michael J. Morowitz
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0036009

Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing
Cited by: 52
Author(s): Xuejian Xiong, Daniel N. Frank, Charles E. Robertson, Stacy Hung, Janet Markle, Angelo J. Canty, Kathy D. McCoy, Andrew J. Macpherson, Philippe Poussier, Jayne S. Danska, John Parkinson
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0012411

Comparative Genomics of Gardnerella vaginalis Strains Reveals Substantial Differences in Metabolic and Virulence Potential
Cited by: 116
Author(s): Carl J. Yeoman, Süleyman Yıldırım, Susan M. Thomas, A. Scott Durkin, Manolito Torralba, Granger Sutton, Christian Buhay, Yan Ding, Shannon Dugan-Rocha, Donna M. Muzny, Xiang Qin, Richard A. Gibbs, Steven R. Leigh, Rebecca M. Stumpf, Bryan A. White, Sarah K. Highlander, Karen E. Nelson, Brenda A. Wilson
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0058563

Genome and Transcriptome Analyses Provide Insight into the Euryhaline Adaptation Mechanism of Crassostrea gigas
Cited by: 123
Author(s): Jie Meng, Qihui Zhu, Linlin Zhang, Chunyan Li, Li Li, Zhicai She, Baoyu Huang, Guofan Zhang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0021751

Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis
Cited by: 70
Author(s): Eugeni Belda, Laia Pedrola, Juli Peretó, Juan F. Martínez-Blanch, Arnau Montagud, Emilio Navarro, Javier F. Urchueguı́a, Daniel Ramón, Andrés Moya, Manuel Porcar
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0075653

Diatom Proteomics Reveals Unique Acclimation Strategies to Mitigate Fe Limitation
Cited by: 68
Author(s): Brook L. Nunn, Jessica F. Faux, Anna A. Hippmann, Maria T. Maldonado, H. Rodger Harvey, David R. Goodlett, Philip W. Boyd, Robert F. Strzepek
Software Mentions: 1
Published: about 11 years ago

10.1128/mSystems.00426-21

Serine Metabolism Tunes Immune Responses To Promote Oreochromis niloticus Survival upon Edwardsiella tarda Infection
Cited by: 21
Author(s): Dai-xiao Yang, Meisongzhu Yang, Yue Yin, Tian-shun Kou, Liao-tian Peng, Zhuang‐Gui Chen, Jun Zheng, Bo Peng
Software Mentions: 1
Published: about 3 years ago

Projects: bioconductor: iPath

Papers Mentioning iPath 95